PDBsum entry 1oop

Virus

PDB id: 1oop

Contents

Protein chains

271 a.a. *

252 a.a. *

238 a.a. *

58 a.a. *

Ligands

SPH

MYR

* Residue conservation analysis

PDB id:

1oop

Name:

Virus

Title:

The crystal structure of swine vesicular disease virus

Structure:

Coat protein vp1. Chain: a. Coat protein vp2. Chain: b. Coat protein vp3. Chain: c. Coat protein vp4. Chain: d

Source:

Swine vesicular disease virus (strain ukg/27/72). Organism_taxid: 12077. Strain: ukg-27-72. Strain: ukg-27-72

Resolution:

3.00Å R-factor: 0.245

Authors:

E.E.Fry,N.J.Knowles,J.W.I.Newman,G.Wilsden,Z.Rao,A.M.Q.King, D.I.Stuart

Key ref:

E.E.Fry et al. (2003). Crystal structure of Swine vesicular disease virus and implications for host adaptation. J Virol, 77, 5475-5486. PubMed id: 12692248

Date:

04-Mar-03 Release date: 22-Apr-03

Protein chain

P13900  (POLG_SVDVU) -  Genome polyprotein from Swine vesicular disease virus (strain UKG/27/72)

Seq: 2185 a.a.

Struc: 271 a.a.*

Protein chain

P13900  (POLG_SVDVU) -  Genome polyprotein from Swine vesicular disease virus (strain UKG/27/72)

Seq: 2185 a.a.

Struc: 252 a.a.

Protein chain

P13900  (POLG_SVDVU) -  Genome polyprotein from Swine vesicular disease virus (strain UKG/27/72)

Seq: 2185 a.a.

Struc: 238 a.a.

Protein chain

P13900  (POLG_SVDVU) -  Genome polyprotein from Swine vesicular disease virus (strain UKG/27/72)

Seq: 2185 a.a.

Struc: 58 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B, C, D: E.C.3.4.22.28 - picornain 3C.
• Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 4: Chains A, B, C, D: E.C.3.4.22.29 - picornain 2A.
• Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 5: Chains A, B, C, D: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

J Virol 77:5475-5486 (2003)

PubMed id: 12692248

Crystal structure of Swine vesicular disease virus and implications for host adaptation.

E.E.Fry, N.J.Knowles, J.W.Newman, G.Wilsden, Z.Rao, A.M.King, D.I.Stuart.

ABSTRACT

Swine vesicular disease virus (SVDV) is an Enterovirus of the family Picornaviridae that causes symptoms indistinguishable from those of foot-and-mouth disease virus. Phylogenetic studies suggest that it is a recently evolved genetic sublineage of the important human pathogen coxsackievirus B5 (CBV5), and in agreement with this, it has been shown to utilize the coxsackie and adenovirus receptor (CAR) for cell entry. The 3.0-A crystal structure of strain UK/27/72 SVDV (highly virulent) reveals the expected similarity in core structure to those of other picornaviruses, showing most similarity to the closest available structure to CBV5, that of coxsackievirus B3 (CBV3). Features that help to cement together and rigidify the protein subunits are extended in this virus, perhaps explaining its extreme tolerance of environmental factors. Using the large number of capsid sequences available for both SVDV and CBV5, we have mapped the amino acid substitutions that may have occurred during the supposed adaptation of SVDV to a new host onto the structure of SVDV and a model of the SVDV/CAR complex generated by reference to the cryo-electron microscopy-visualized complex of CBV3 and CAR. The changes fall into three clusters as follows: one lines the fivefold pore, a second maps to the CAR-binding site and partially overlaps the site for decay accelerating factor (DAF) to bind to echovirus 7 (ECHO7), and the third lies close to the fivefold axis, where the low-density lipoprotein receptor binds to the minor group of rhinoviruses. Later changes in SVDV (post-1971) map to the first two clusters and may, by optimizing recognition of a pig CAR and/or DAF homologue, have improved the adaptation of the virus to pigs.